Although small-scale cell culture has been around for about a century, the notion of culturing cells on a large scale is only a decade old, invented out of the necessity to accommodate the growing commercial success of biotech-based therapeutics, mostly monoclonal antibodies and small peptide-sized molecules.
The industrial route for making protein drugs inside cells is fairly well established, even at the relatively callow age of ten. In the general paradigm, a gene for a therapeutic protein is inserted into a cell—the most popular mammalian cell for industrial purposes being a line of Chinese hamster ovary (CHO) cells. Great quantities—thousands of liters—of the genetically engineered CHO cells are cultured, fed, and nurtured and encouraged to undergo successive cell divisions to make yet more cells, which, of course, are also producing large quantities of the therapeutic protein. The therapeutic protein is secreted from the cells, or the cells are later cracked open so the therapeutic protein can be extracted and purified from them, formulated, packaged, and then sold as a drug.
Treating the cells badly means that rather than allowing them to rest on a solid substrate, as most cells "prefer," cells grown for bioprocessing are suspended in a kind of nutritive broth called medium. The suspension is contained inside either a large stainless-steel vat or a large plastic (and therefore disposable) bioreactor and somehow rocked or churned or mixed to make sure that all cells have equal access to the nutrients and gases dissolved within the medium. Because they're suspended in huge vats or bags, and because they're being roiled around, the cells ball up and bump up against each other and against the vessel in which they're growing. And, as Mason noted, this harsh treatment—destructive to many cells—is fine, because the cells are not the end game. They're not the product.